binaries/src/ViennaRNA/doc/html/snofold_8h_source.html

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  68 <h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/snofold.h</h1><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/* function from fold.c */</span>
  69 <a name="l00002"></a>00002 <span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_SNOFOLD_H__</span>
  70 <a name="l00003"></a>00003 <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_SNOFOLD_H__</span>
  71 <a name="l00004"></a>00004 <span class="preprocessor"></span>
  72 <a name="l00005"></a>00005 <span class="preprocessor">#include &quot;<a class="code" href="data__structures_8h.html" title="All datastructures and typedefs shared among the Vienna RNA Package can be found...">data_structures.h</a>&quot;</span>
  73 <a name="l00006"></a>00006
  74 <a name="l00007"></a>00007 <span class="comment">/* Normal fold */</span>
  75 <a name="l00008"></a>00008
  76 <a name="l00012"></a>00012 <span class="keywordtype">int</span>  snofold( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,
  77 <a name="l00013"></a>00013     <span class="keywordtype">char</span> *structure,
  78 <a name="l00014"></a>00014                 <span class="keyword">const</span> <span class="keywordtype">int</span> max_assym,
  79 <a name="l00015"></a>00015                 <span class="keyword">const</span> <span class="keywordtype">int</span> threshold,
  80 <a name="l00016"></a>00016                 <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,
  81 <a name="l00017"></a>00017                 <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,
  82 <a name="l00018"></a>00018                 <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,
  83 <a name="l00019"></a>00019                 <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem);
  84 <a name="l00024"></a>00024 <span class="keywordtype">void</span>   snofree_arrays(<span class="keyword">const</span> <span class="keywordtype">int</span> length);  <span class="comment">/* free arrays for mfe folding */</span>
  85 <a name="l00025"></a>00025 <span class="keywordtype">void</span>   snoinitialize_fold(<span class="keywordtype">int</span> length);    <span class="comment">/* allocate arrays for folding */</span>
  86 <a name="l00026"></a>00026 <span class="keywordtype">void</span>   snoupdate_fold_params(<span class="keywordtype">void</span>);       <span class="comment">/* recalculate parameters */</span>
  87 <a name="l00027"></a>00027 <span class="keywordtype">int</span>    snoloop_energy(<span class="keywordtype">short</span> *ptable,
  88 <a name="l00028"></a>00028                       <span class="keywordtype">short</span> *s,
  89 <a name="l00029"></a>00029                       <span class="keywordtype">short</span> *s1,
  90 <a name="l00030"></a>00030                       <span class="keywordtype">int</span> i);
  91 <a name="l00031"></a>00031 <span class="keywordtype">void</span>   snoexport_fold_arrays( <span class="keywordtype">int</span> **indx_p,
  92 <a name="l00032"></a>00032                               <span class="keywordtype">int</span> **mLoop_p,
  93 <a name="l00033"></a>00033                               <span class="keywordtype">int</span> **cLoop,
  94 <a name="l00034"></a>00034                               <a class="code" href="structfolden.html">folden</a> ***fold_p,
  95 <a name="l00035"></a>00035                               <a class="code" href="structfolden.html">folden</a> ***fold_p_XS);
  96 <a name="l00036"></a>00036 <span class="keywordtype">char</span> * snobacktrack_fold_from_pair( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,
  97 <a name="l00037"></a>00037                                     <span class="keywordtype">int</span> i,
  98 <a name="l00038"></a>00038                                     <span class="keywordtype">int</span> j);
  99 <a name="l00039"></a>00039 <span class="comment">/* alifold */</span>
 100 <a name="l00040"></a>00040 <span class="keywordtype">float</span> alisnofold( <span class="keyword">const</span> <span class="keywordtype">char</span> **strings,
 101 <a name="l00041"></a>00041                   <span class="keyword">const</span> <span class="keywordtype">int</span> max_assym,
 102 <a name="l00042"></a>00042                   <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop,
 103 <a name="l00043"></a>00043                   <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,
 104 <a name="l00044"></a>00044                   <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,
 105 <a name="l00045"></a>00045                   <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,
 106 <a name="l00046"></a>00046                   <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem);
 107 <a name="l00047"></a>00047 <span class="keywordtype">void</span>  alisnofree_arrays(<span class="keyword">const</span> <span class="keywordtype">int</span> length);
 108 <a name="l00048"></a>00048 <span class="keywordtype">char</span>  *alisnobacktrack_fold_from_pair(<span class="keyword">const</span> <span class="keywordtype">char</span> **sequence,
 109 <a name="l00049"></a>00049                                       <span class="keywordtype">int</span> i,
 110 <a name="l00050"></a>00050                                       <span class="keywordtype">int</span> j,
 111 <a name="l00051"></a>00051                                       <span class="keywordtype">int</span> *cov);
 112 <a name="l00052"></a>00052 <span class="keyword">extern</span> <span class="keywordtype">double</span> <a class="code" href="group__consensus__fold.html#gaf3cbac6ff5d706d6e414677841ddf94c" title="This variable controls the weight of the covariance term in the energy function of...">cv_fact</a> <span class="comment">/* =1 */</span>;
 113 <a name="l00053"></a>00053 <span class="keyword">extern</span> <span class="keywordtype">double</span> <a class="code" href="group__consensus__fold.html#ga502948a122a2af5b914355b1f3ea2f61" title="This variable controls the magnitude of the penalty for non-compatible sequences...">nc_fact</a> <span class="comment">/* =1 */</span>;
 114 <a name="l00054"></a>00054
 115 <a name="l00055"></a>00055 <span class="comment">/* max number of mismatch &gt;&gt;&gt;&gt;&gt;..((   )).&gt;&gt;&gt;&gt; */</span>
 116 <a name="l00056"></a>00056 <span class="preprocessor">#define MISMATCH 3</span>
 117 <a name="l00057"></a>00057 <span class="preprocessor"></span>
 118 <a name="l00058"></a>00058 <span class="preprocessor">#endif</span>
 119 </pre></div></div>
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